Variant report

Variant	rs7135791
Chromosome Location	chr12:48159721-48159722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48107776..48110722-chr12:48159579..48161577,2	K562	blood:
2	chr12:48151685..48153406-chr12:48157553..48160155,2	K562	blood:
3	chr12:48137468..48138958-chr12:48159470..48161629,19	MCF-7	breast:
4	chr12:48135637..48139273-chr12:48158658..48160407,3	MCF-7	breast:
5	chr12:48126300..48127984-chr12:48159305..48162303,2	K562	blood:
6	chr12:48146396..48149240-chr12:48159441..48161516,3	MCF-7	breast:
7	chr12:48159584..48163240-chr12:48212349..48215466,3	MCF-7	breast:
8	chr12:48136675..48140577-chr12:48159168..48161619,5	MCF-7	breast:
9	chr12:48121380..48124034-chr12:48159649..48162276,2	MCF-7	breast:
10	chr12:48151780..48155631-chr12:48159603..48164338,5	MCF-7	breast:
11	chr12:48154545..48157015-chr12:48158766..48160780,2	MCF-7	breast:
12	chr12:48153850..48156955-chr12:48157657..48160878,3	K562	blood:
13	chr12:48158914..48160973-chr12:48211450..48214285,2	K562	blood:
14	chr12:48159551..48161566-chr12:48212867..48215590,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1006476	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1006477	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168244	1.00[LWK][hapmap]
rs58067800	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59205218	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60776348	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7136720	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7306788	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7307367	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73291230	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs734706	0.89[GIH][hapmap]
rs7488942	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7959510	0.94[CEU][hapmap];0.85[GIH][hapmap]
rs7964310	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs875023	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7135791	BCDIN3D	cis	cerebellum	SCAN
rs7135791	OR5D13	trans	parietal	SCAN
rs7135791	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48153400-48161800	Weak transcription	Aorta	Aorta
2	chr12:48153600-48159800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:48153600-48161000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:48153600-48161200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:48153600-48161200	Weak transcription	NHDF-Ad	bronchial
6	chr12:48153600-48162000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:48153600-48162200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:48153600-48162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:48153600-48166000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:48153600-48166200	Weak transcription	Brain Anterior Caudate	brain
11	chr12:48153600-48166400	Weak transcription	Fetal Brain Female	brain
12	chr12:48153600-48166800	Weak transcription	Gastric	stomach
13	chr12:48153800-48161400	Weak transcription	K562	blood
14	chr12:48153800-48162000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:48153800-48162200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:48153800-48165600	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:48153800-48165800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:48153800-48166200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:48154200-48161200	Weak transcription	A549	lung
20	chr12:48154200-48161200	Weak transcription	Hela-S3	cervix
21	chr12:48154400-48165800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:48156400-48159800	Enhancers	Right Ventricle	heart
23	chr12:48156400-48160200	Enhancers	Fetal Heart	heart
24	chr12:48156400-48161600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:48156800-48160200	Enhancers	HMEC	breast
26	chr12:48156800-48163400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:48157200-48162400	Enhancers	Fetal Thymus	thymus
28	chr12:48157600-48160800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:48157600-48164200	Weak transcription	Fetal Lung	lung
30	chr12:48157800-48160600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:48157800-48160600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:48157800-48161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:48157800-48162000	Weak transcription	Ovary	ovary
34	chr12:48157800-48165800	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:48157800-48166200	Weak transcription	Lung	lung
36	chr12:48157800-48166200	Weak transcription	Right Atrium	heart
37	chr12:48158000-48159800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:48158000-48160000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:48158200-48160600	Weak transcription	Primary B cells from cord blood	blood
40	chr12:48158200-48164800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:48158200-48166600	Weak transcription	Fetal Kidney	kidney
42	chr12:48158400-48160600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:48158400-48163800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:48158400-48164400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:48158600-48164800	Enhancers	NHEK	skin
46	chr12:48158800-48160200	Enhancers	Stomach Smooth Muscle	stomach
47	chr12:48159000-48159800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:48159000-48159800	Enhancers	Rectal Smooth Muscle	rectum
49	chr12:48159000-48160200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:48159000-48160200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links